Generate phylogenomic tree from aligment file.
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As mentioned in the phylogenetics tutorial, it currently only has the option to use FastTree to do so, but be aware that there are many other programs that you can do this with. Some of the options we are familiar with (and are not yet represented in
anvi-gen-phylogenomic-tree) include MrBayes, MEGA, and PHYLIP, among many others, most of which will happily take a concatenated-gene-alignment-fasta.
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Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the
__resources__ tag in this file to see an example.